The possibility of increasing the working temperature of fuel cells using Nafion as ionomer membranes by a new annealing procedure in the presence of dimethylsulfoxide or tributylphosphate as annealing agents has been investigated. The extent of annealing was derived by the shift of nc/T plots of annealed membranes (nc is the index of counter-elastic force) relatively to the plot of as received membranes. nc/T plots can be used as a powerful analytical method useful for deriving quantitative information on the annealing extent and for obtaining information on the melting temperature of the semi-crystalline phase grown during annealing. It was found that, by using an annealing temperature of 140 °C in the presence of an annealing agent, an important effect on the thermal stability of Nafion membranes was obtained. The increased thermal stability was related to the increase of the original semi-crystalline phase which acts as a physical cross-linker so that the mechanical properties are no longer lost at the glass transition temperature but at the melting point of the semi-crystalline phase. The use of nc/T plots as analytical tools for detecting and understanding important ionomer properties was denominated as “Ionomer nc Analysis” (INCA).